The purpose of smoothing is to reduce the number of false peaks detected by the software. Prior to GeneMapper^® ID 3.2, the Macintosh GS software smoothed before the data were analyzed and the GS software for Windows NT smoothed after analysis. This particular difference in the smoothing algorithm between Macintosh and Windows NT versions produced slightly different peak heights for the same sample files. When working with an established threshold, this could cause differences in allele designations.

The algorithm used for GS 3.7.1 for Windows NT (the updater) also tends to increase baseline noise, but operating with GS 3.7 for Windows NT gave similar results for peak height as that of the Macintosh version. A thorough discussion of each of the parameter settings shown above can be found in the User Bulletin of the Windows NT software for GeneScan^®.⁰⁵

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